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Salinity is known to be a driving factor in defining habitat suitability for estuarine-dependent species. With increased demands placed on freshwater resources and extreme drought conditions becoming prevalent for many coastal regions, it is important to understand how these changes may impact the extent and distribution of suitable habitat for species that rely on the passage of freshwater to the coastal region. Here, habitat suitability models were constructed for three estuarine species (Farfantepenaeus aztecus, Micropogonias undulatus, and Cynoscion nebulosus) across three estuary classes (based on freshwater balance: positive, neutral, and negative estuaries) and for three simulated salinity regimes (low, moderate, and high salinities). The impact of changing salinity regimes on habitat suitability varied most notably at the species level but also varied significantly across the three estuary types examined. Of the three species examined, F. aztecus showed relatively little salinity-related variation in habitat extent or distribution. Variation in M. undulatus and C. nebulosus salinity impact was especially clear in relatively neutral and positive estuaries where distribution of habitat within the estuary under the varying salinity regimes followed intra-estuarine salinity gradients to match salinity preference for each species and typically resulted in a gradual shrinking of highly suitable habitat area into the far upper estuary as salinities increased. While salinity was not found to be the only or even the most impactful of variables regarding habitat suitability, model outputs show that at the estuary scale, salinity can have substantial influence on the spatial extent and distribution of suitable habitat and this influence is not constant across estuary types. Modeling exercises such as this are the first step in communicating such impacts and focusing the vigilance of resource managers towards vulnerable species and habitat regions.